It is something else in the document class that is determining this behavior. Please post a minimal working example to proceed further. Even the name of the document class you're using (or even the name of the class it is based on, if there is such a thing) would help.

when I tested it, also with svjour3 the problem doesn't happen. So there's something in your code which you did not show. Please have a look at the web site Karl and Svend linked to, to learn why a minimal example is important and nearly a guarantee for getting a solution.

Actually, I also just found the solution (well, sort of). I went into the svjour3 cls file and found where the equations in two column mode are default set "fleqn" (line 42 of the code I believe). Just delete the "fleqn" inside the curly brackets , {}, and you'll get centered equations. Again, this is in the svjour3 style file itself that this must be done.

I got the same issue with equation environment. In two-column document it does not center properly, in one-column document it stays fine. Deleting 'fleqn' from line #42 in svjour3.cls helps, thank you. Do you have any idea whether this can be solved within the source .tex? It is not a problem if I compile the document myself with my own svjour3.cls, but if the journal administration does it, I won't be sure whether they will use svjour3.cls with 'fleqn' removed. I will contact the publisher on this but I'm not sure how fast they will respond on such request.